National Autonomous University of Mexico

About: National Autonomous University of Mexico is a education organization based out in Mexico City, Distrito Federal, Mexico. It is known for research contribution in the topics: Population & Galaxy. The organization has 72868 authors who have published 127797 publications receiving 2285543 citations. The organization is also known as: UNAM & Universidad Nacional Autónoma de México.

A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples

Abstract: Unbiased next-generation sequencing (NGS) approaches enable comprehensive pathogen detection in the clinical microbiology laboratory and have numerous applications for public health surveillance, outbreak investigation, and the diagnosis of infectious diseases. However, practical deployment of the technology is hindered by the bioinformatics challenge of analyzing results accurately and in a clinically relevant timeframe. Here we describe SURPI ("sequence-based ultrarapid pathogen identification"), a computational pipeline for pathogen identification from complex metagenomic NGS data generated from clinical samples, and demonstrate use of the pipeline in the analysis of 237 clinical samples comprising more than 1.1 billion sequences. Deployable on both cloud-based and standalone servers, SURPI leverages two state-of-the-art aligners for accelerated analyses, SNAP and RAPSearch, which are as accurate as existing bioinformatics tools but orders of magnitude faster in performance. In fast mode, SURPI detects viruses and bacteria by scanning data sets of 7-500 million reads in 11 min to 5 h, while in comprehensive mode, all known microorganisms are identified, followed by de novo assembly and protein homology searches for divergent viruses in 50 min to 16 h. SURPI has also directly contributed to real-time microbial diagnosis in acutely ill patients, underscoring its potential key role in the development of unbiased NGS-based clinical assays in infectious diseases that demand rapid turnaround times.

Infection and mortality of healthcare workers worldwide from COVID-19: a systematic review.

Abstract: Objectives To estimate COVID-19 infections and deaths in healthcare workers (HCWs) from a global perspective during the early phases of the pandemic. Design Systematic review. Methods Two parallel searches of academic bibliographic databases and grey literature were undertaken until 8 May 2020. Governments were also contacted for further information where possible. There were no restrictions on language, information sources used, publication status and types of sources of evidence. The AACODS checklist or the National Institutes of Health study quality assessment tools were used to appraise each source of evidence. Outcome measures Publication characteristics, country-specific data points, COVID-19-specific data, demographics of affected HCWs and public health measures employed. Results A total of 152 888 infections and 1413 deaths were reported. Infections were mainly in women (71.6%, n=14 058) and nurses (38.6%, n=10 706), but deaths were mainly in men (70.8%, n=550) and doctors (51.4%, n=525). Limited data suggested that general practitioners and mental health nurses were the highest risk specialities for deaths. There were 37.2 deaths reported per 100 infections for HCWs aged over 70 years. Europe had the highest absolute numbers of reported infections (119 628) and deaths (712), but the Eastern Mediterranean region had the highest number of reported deaths per 100 infections (5.7). Conclusions COVID-19 infections and deaths among HCWs follow that of the general population around the world. The reasons for gender and specialty differences require further exploration, as do the low rates reported in Africa and India. Although physicians working in certain specialities may be considered high risk due to exposure to oronasal secretions, the risk to other specialities must not be underestimated. Elderly HCWs may require assigning to less risky settings such as telemedicine or administrative positions. Our pragmatic approach provides general trends, and highlights the need for universal guidelines for testing and reporting of infections in HCWs. © Author(s) (or their employer(s)) 2020.

A comparative study of disc–planet interaction

Abstract: We perform numerical simulations of a disc-planet system using various grid-based and smoothed particle hydrodynamics (SPH) codes. The tests are run for a simple setup where Jupiter and Neptune mass planets on a circular orbit open a gap in a protoplanetary disc during a few hundred orbital periods. We compare the surface density contours, potential vorticity and smoothed radial profiles at several times. The disc mass and gravitational torque time evolution are analysed with high temporal resolution. There is overall consistency between the codes. The density profiles agree within about 5 per cent for the Eulerian simulations. The SPH results predict the correct shape of the gap although have less resolution in the low-density regions and weaker planetary wakes. The disc masses after 200 orbital periods agree within 10 per cent. The spread is larger in the tidal torques acting on the planet which agree within a factor of 2 at the end of the simulation. In the Neptune case, the dispersion in the torques is greater than for Jupiter, possibly owing to the contribution from the not completely cleared region close to the planet.

The chandra cosmos legacy survey: overview and point source catalog

Abstract: The COSMOS-Legacy survey is a 4.6 Ms Chandra program that has imaged 2.2 deg2 of the COSMOS field with an effective exposure of ≃ 160 ks over the central 1.5 deg^2 and of ≃ 80 ks in the remaining area. The survey is the combination of 56 new observations obtained as an X-ray Visionary Project with the previous C-COSMOS survey. We describe the reduction and analysis of the new observations and the properties of 2273 point sources detected above a spurious probability of 2 × 10^(−5). We also present the updated properties of the C-COSMOS sources detected in the new data. The whole survey includes 4016 point sources (3814, 2920 and 2440 in the full, soft, and hard band). The limiting depths are 2.2 × 10^(−16), 1.5 × 10^(−15), and 8.9 × 10^(−16) erg cm^(-2)s^(-1) in the 0.5–2, 2–10, and 0.5–10 keV bands, respectively. The observed fraction of obscured active galactic nuclei with a column density >10^(22) cm^(−2) from the hardness ratio (HR) is 50_(-16)^(+17)%. Given the large sample we compute source number counts in the hard and soft bands, significantly reducing the uncertainties of 5%–10%. For the first time we compute number counts for obscured (HR > −0.2) and unobscured (HR < −0.2) sources and find significant differences between the two populations in the soft band. Due to the unprecedent large exposure, COSMOS-Legacy area is three times larger than surveys at similar depths and its depth is three times fainter than surveys covering similar areas. The area-flux region occupied by COSMOS-Legacy is likely to remain unsurpassed for years to come.